MolNFT v1 · #143925 · protein
ADAM10 extracellular domain bound by the 11G2 Fab
6BDZ · 11G2 Fab light chain: “ADAM10 extracellular domain bound by the 11G2 Fab”. X-ray diffraction, 5 ligands (NAG, MAN, CA), 5 pockets (best druggability 0.75). MolNFT v1 #143925 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BDZ
- Type
- protein
- Length
- 855 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 11G2 Fab light chain; 11G2 Fab heavy chain; Disintegrin and metalloproteinase…
- EC
- 3.4.24.81
- UniProt
- O14672
- Ligands
- NAG, MAN, CA, ZN, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 11G2 Fab light chain | protein | 215 | 6% helix, 54% strand | — |
| H | 11G2 Fab heavy chain | protein | 219 | 5% helix, 48% strand | — |
| A | Disintegrin and metalloproteinase domain-containing protein 10 (EC 3.4.24.81) | protein | 421 | 23% helix, 15% strand | O14672 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains L, H, A
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains H, L, A
- CA · Calcium ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.75 | 0.78 | 105 | empty |
| 2 | 474 | 0.61 | 0.75 | 60 | empty |
| 3 | 182 | 0.58 | 0.82 | 27 | ZN |
| 4 | 291 | 0.57 | 0.77 | 41 | empty |
| 5 | 75 | 0.39 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2033 Ų buried · 21 hydrogen bonds · protein-protein
- H–A · 535 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 261 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 3 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6BDZ · ADAM10 Extracellular Domain Bound by the 11G2 Fab · the same entry in another collection · chain L against L, TM-score 1.00
- O14672 · AlphaFold monomer V2.0 prediction for disintegrin and metalloproteinase domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.59
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O14672
- Elsewhere: RCSB PDB 6BDZ · PDBe 6BDZ · UniProt O14672
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